biobakery / biobakery_workflows

bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.
http://huttenhower.sph.harvard.edu/biobakery_workflows
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TypeError: object of type 'dict_keyiterator' has no len() #29

Closed jowodo closed 2 years ago

jowodo commented 2 years ago

Dear developers, I'm trying to install on a HPC:

I tried to execute with the example data form this repository:

biobakery_workflows wmgx \
        --input biobakery_workflows/examples/wmgx/paired \
        --output outdir \
        --bypass-strain-profiling

but always I get this error:

Traceback (most recent call last):
  File "/apps/biobakery-workflows/3.0.0a7/bin/wmgx.py", line 184, in <module>
    workflow.go()
  File "/apps/biobakery-workflows/3.0.0a7/lib/python3.9/site-packages/anadama2/workflow.py", line 800, in go
    _runner.run_tasks(task_idxs)
  File "/apps/biobakery-workflows/3.0.0a7/lib/python3.9/site-packages/anadama2/runners.py", line 141, in run_tasks
    self.ctx._handle_task_started(idx)
  File "/apps/biobakery-workflows/3.0.0a7/lib/python3.9/site-packages/anadama2/workflow.py", line 884, in _handle_task_started
    self._reporter.task_started(task_no)
  File "/apps/biobakery-workflows/3.0.0a7/lib/python3.9/site-packages/anadama2/reporters.py", line 196, in task_started
    r.task_started(task_no)
  File "/apps/biobakery-workflows/3.0.0a7/lib/python3.9/site-packages/anadama2/reporters.py", line 641, in task_started
    self.log_event("ready and waiting for resources", task_no, self._daginfo(task_no))
  File "/apps/biobakery-workflows/3.0.0a7/lib/python3.9/site-packages/anadama2/reporters.py", line 597, in _daginfo
    return msg.format(len(parents), parents, len(children), children)
TypeError: object of type 'dict_keyiterator' has no len()

I don't know how to troubleshoot. Any direction, hint or idea would be welcome. I couldn't find any related issues here, on the anadama2 github page or the biobakery forum

Thanks

github-actions[bot] commented 2 years ago

Thank you for creating this issue. We currently field issues through our bioBakery Discourse Support Forum. If you would please post the issue to discourse we would be happy to sync up with you to get it resolved.